Hopkins began riding Motocross bikes as a child and won his first race on a MiniBike on 1986, switching to road racing full-time in 1999. Hopkins proposed to his girlfriend Ashleigh in the summer of 2007 on her 21st birthday. They married in Las Vegas in December 2007.

The 2002 season saw Hopkins join the WCM RedBull Yamaha team alongside multiple race winner Garry McCoy. The team was using Yamaha YZR500 motorcycles on lease from Yamaha. Overall the YZR500 was considered to be uncompetitive that year, due to a change in the regulations allowing 990 cc four-stroke motorcycles to race against 500 cc two-stroke motorcycles. Although the two-strokes held (on average) a 10 kg weight advantage over the four-strokes, they had between 30 and 50 less hp depending on the engine configuration used for the racetrack. Hopkins finished the season ranked 15th, with 58 points, which put him 25 points clear of his teammate McCoy.

In 2003 Hopkins joined the Suzuki factory racing team. This year he would ride a 990 cc V4 four-stroke. In 2003 John was teamed with 2000500cc world championKenny Roberts, Jr.. Although he was racing a four-stroke this year, the results did not seem to come as one would have expected. There are many theories for this, including the Suzuki's lack of power and its tendency to wear out tires faster than other bikes. This year also saw Hopkins involved in a turn 1 crash at the Japanese Grand Prix at Motegi, he was accused of causing this crash, and was suspended for one race. This suspension resulted in a DNS (did not start) at the Malaysian Grand Prix. Also noteworthy for the 2003 season was the crash in Italy where Kenny Roberts, Jr.'s GSV-R Suzuki suffered an engine management failure and the bike launched into Hopkins, putting both GSV-R's out of the race. At the end of the season, Hopkins finished in 17th place with 29 points. This finish put him 2 places and 7 points ahead of his teammate Kenny Roberts, Jr.

The technology and technical advancement of the GSV-R was further developed in 2004. Most of the refinements took place in the engine management package, making the bike easier to ride. Towards the end of the year, the GSV-R was showing clear improvements, allowing Hopkins to move up the standings. Unfortunately it also saw several mechanical failures, which effectively undid the hard work to develop the motorcycle. Having qualified on the front row at Motegi, he was eliminated in a first-corner crash. Of note is that John was crashed into by Loris Capirossi, one of the same riders he himself had hit at the very same turn 1 at Motegi in 2003. Overall he finished 16th.

John continued with Suzuki in 2005, as the team showed promising signs after the arrival of Paul Denning as team boss following Denning's success with Suzuki's British Superbike team. John briefly led at Donington, but his best result was a 5th place at Motegi, and he was 14th overall. Qualifying results were often better than race results, largely due to Bridgestone tires being better suited to short runs.

Remains at Suzuki, now backed by Rizla, where he is joined by new team-mate Chris Vermeulen. Enjoys his best season yet. Hopkins finished the 2006 season in 10th place overall with 116 points. Hopkins has had one pole position this season, at Assen. His best finishes were in China and in Catalunya, where he finished fourth.

Continuing with Rizla Suzuki, Hopkins set near-lap-record times aboard the new 800 cc motorcycle, and was labeled the dark horse by Colin Edwards. On February 15, 2007 he fractured his wrist after falling while testing at the Jerez circuit in Spain, but returned for the start of the season.

Hopkins completed his first MotoGP podium finish at the Shanghai circuit in China, finishing in 3rd place – 3.6 seconds behind Valentino Rossi but 7.6 seconds ahead of 2006 event winner Dani Pedrosa. He finished as 4th overall in the 2007 season, two places ahead of Vermeulen and one behind Rossi.

For 2008 he joins Kawasaki Racing Team. Explaining the decision, Rizla Suzuki boss Paul Denning suggested that "There are reasons for that other than performance."[4] He crashed heavily at Assen, fracturing his ankle.

Prior to 2009 season, Kawasaki made the decision to halt MotoGP racing activities because of the global economic crisis, meaning that John Hopkins would not have a ride for the 2009 season.

After the Kawasaki team pulling out of MotoGP, Hopkins secured a mid season ride on the Stiggy Racing Honda[6] Replacing the sacked Roberto Rolfo. Hopkins scored points during his first round in Valencia. At the next round in Assen Hopkins would fall and dislocate his hip, Hopkins then wouldn't return until San Marino [7] where he couldn't complete the weekends racing. After a career best finish in the first race at Donington Hopkins who was still hurt couldn't complete the second race. Following 2 retirements at the Brno round, Hopkins would suffer a horror crash and the Nürburgring being run over after he was taken out by Makoto Tamada and Broc Parkes, Hopkins was unconscious for ten minutes but luckily sustained no serious injuries.[8] The Stiggy Honda team then withdrew from the world superbike paddock leaving Hopkins once again without a ride for 2010.[9]

In 2011 Hopkins rode his Samsung Crescent Suzuki at the Silverstone World Superbike round. Hopkins was fast from the start being fastest in free practice sessions, capturing his first Superbike World Championship pole position with a new circuit record lap.[10]

In October 2012, Hopkins announced that he would be taking the 2013 season off to recover from his injuries.[11] In April 2013, Hopkins had hip replacement surgery following a heavy crash at Monza, but announced at the Le Mans MotoGP event in May that he would be testing again within two months. [12]

For the 2011 season Hopkins raced in the British Superbike Championship. He rode for the Crescent Suzuki team. At Oulton Park he won the second race making history, being the first American to win a British Superbike race. Hopkins made history yet again at the new Snetterton 300 where he won the first British Superbike race.

Hopkins came within 0.006 seconds of winning the title. Losing out to Tommy Hill on the last lap of the final round at Brands Hatch.

On the 29th of October 2013 it was announced that Hopkins, after taking a year out to recover from multiple injuries, would return to the British Superbike Championship for 2014 having signed to ride for Tyco Suzuki.

1.^ – Hopkins was not entered for the Cadwell race due to an injury he sustained during his wildcard ride for Suzuki at the Moto GP event in Brno.[18]

2.^ – Hopkins qualified for "The Showdown" part of the BSB season, thus before the Donington Park round he was awarded 500 points plus the podium credits he had gained throughout the season. Podium credits are given to anyone finishing 1st, 2nd or 3rd, with 3,2 and 1 points awarded respectively.